Updating benchtop sequencing performance comparison

Jünemann, Sebastian; Sedlazeck, Fritz J.; Prior, Karola; Albersmeier, Andreas; John, Uwe; Kalinowski, Jörn; Mellmann, Alexander; Goesmann, Alexander; Haeseler, Arndt von; Stoye, Jens; Harmsen, Dag

doi:10.1038/nbt.2522

Cited by 384 publications

(291 citation statements)

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“…Furthermore, there were some false positive INDEL, as previously reported by other Ion Torrent sequencing users. [26][27][28] These could be addressed by re-designing primers covering that particular VHL genomic region, optimizing the variant calling bioinformatics workflow and employing recently proposed strategies to increase the accuracy of INDEL detection. 26,28 Another limitation of the panel -related to the nature of its technology -is that it can only identify SNV and short INDEL but not other structural variants such as large INDEL or copy number variations.…”

Section: Discussionmentioning

confidence: 99%

Gene panel sequencing improves the diagnostic work-up of patients with idiopathic erythrocytosis and identifies new mutations

et al. 2016

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Section: Discussionmentioning

confidence: 99%

Gene panel sequencing improves the diagnostic work-up of patients with idiopathic erythrocytosis and identifies new mutations

et al. 2016

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“…For clinical MTBC isolates, three classical genotyping techniques have been used during the last few years, IS6110 restriction fragment length polymorphism (RFLP) typing, spoligotyping (clustered regularly interspaced palindromic repeats [CRISPRs]), and mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing of up to 24 loci (7)(8)(9). Classical genotyping has been applied to a variety of research questions ranging from local outbreak analyses and longitudinal molecular epidemiological studies to analysis of global population structure, global spread of particular variants, and host pathogen coevolution (10)(11)(12)(13).…”

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confidence: 99%

Whole-Genome-Based Mycobacterium tuberculosis Surveillance: a Standardized, Portable, and Expandable Approach

et al. 2014

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f Whole-genome sequencing (WGS) allows for effective tracing of Mycobacterium tuberculosis complex (MTBC) (tuberculosis pathogens) transmission. However, it is difficult to standardize and, therefore, is not yet employed for interlaboratory prospective surveillance. To allow its widespread application, solutions for data standardization and storage in an easily expandable database are urgently needed. To address this question, we developed a core genome multilocus sequence typing (cgMLST) scheme for clinical MTBC isolates using the Ridom SeqSphere ؉ software, which transfers the genome-wide single nucleotide polymorphism (SNP) diversity into an allele numbering system that is standardized, portable, and not computationally intensive. To test its performance, we performed WGS analysis of 26 isolates with identical IS6110 DNA fingerprints and spoligotyping patterns from a longitudinal outbreak in the federal state of Hamburg, Germany (notified between 2001 and 2010). The cgMLST approach (3,041 genes) discriminated the 26 strains with a resolution comparable to that of SNP-based WGS typing (one major cluster of 22 identical or closely related and four outlier isolates with at least 97 distinct SNPs or 63 allelic variants). Resulting tree topologies are highly congruent and grouped the isolates in both cases analogously. Our data show that SNP-and cgMLSTbased WGS analyses facilitate high-resolution discrimination of longitudinal MTBC outbreaks. cgMLST allows for a meaningful epidemiological interpretation of the WGS genotyping data. It enables standardized WGS genotyping for epidemiological investigations, e.g., on the regional public health office level, and the creation of web-accessible databases for global TB surveillance with an integrated early warning system.

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“…However, a fundamental limitation of these technologies is the high rate of incorrectly identified DNA bases in the data produced (1,2). For instance, reports in the literature suggest that Illumina sequencing machines produce errors at a rate of ∼0.1-1 × 10 −2 per base sequenced, depending on the data-filtering scheme used (2,3).…”

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confidence: 99%

High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing

Lou¹,

Hussmann²,

McBee³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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A major limitation of high-throughput DNA sequencing is the high rate of erroneous base calls produced. For instance, Illumina sequencing machines produce errors at a rate of ∼0.1-1 × 10 −2 per base sequenced. These technologies typically produce billions of base calls per experiment, translating to millions of errors. We have developed a unique library preparation strategy, "circle sequencing," which allows for robust downstream computational correction of these errors. In this strategy, DNA templates are circularized, copied multiple times in tandem with a rolling circle polymerase, and then sequenced on any high-throughput sequencing machine. Each read produced is computationally processed to obtain a consensus sequence of all linked copies of the original molecule. Physically linking the copies ensures that each copy is independently derived from the original molecule and allows for efficient formation of consensus sequences. The circlesequencing protocol precedes standard library preparations and is therefore suitable for a broad range of sequencing applications. We tested our method using the Illumina MiSeq platform and obtained errors in our processed sequencing reads at a rate as low as 7.6 × 10 −6 per base sequenced, dramatically improving the error rate of Illumina sequencing and putting error on par with low-throughput, but highly accurate, Sanger sequencing. Circle sequencing also had substantially higher efficiency and lower cost than existing barcode-based schemes for correcting sequencing errors.next-generation sequencing | barcoding | rare variants

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Updating benchtop sequencing performance comparison

Cited by 384 publications

References 7 publications

Gene panel sequencing improves the diagnostic work-up of patients with idiopathic erythrocytosis and identifies new mutations

Gene panel sequencing improves the diagnostic work-up of patients with idiopathic erythrocytosis and identifies new mutations

Whole-Genome-Based Mycobacterium tuberculosis Surveillance: a Standardized, Portable, and Expandable Approach

High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing

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